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refgenie / refgenconf

A Python object for standardized reference genome assets.
http://refgenie.databio.org
BSD 2-Clause "Simplified" License
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failed refgenie pull breaks the config #115

Closed stolarczyk closed 3 years ago

stolarczyk commented 3 years ago 
$ refgenie pull dm6/fasta
No local digest for genome alias: dm6
Setting 'dm6' identity with server: http://rg.databio.org/v3/alias/genome_digest/dm6
Determined server digest for local genome alias (dm6): 98190192e366fa1f69d56b75275b1064ec802a9cc85741d0
Set genome alias (98190192e366fa1f69d56b75275b1064ec802a9cc85741d0: dm6)
Created alias directories:
 - /project/shefflab/genomes_V04/alias/dm6
Downloading URL: http://rg.databio.org/v3/asset/98190192e366fa1f69d56b75275b1064ec802a9cc85741d0/fasta/archive
Asset archive '98190192e366fa1f69d56b75275b1064ec802a9cc85741d0/fasta:default' is missing on the server: http://rg.databio.org

results in

  98190192e366fa1f69d56b75275b1064ec802a9cc85741d0:
    aliases: ['dm6']
genome_servers: ['http://rg.databio.org']
stolarczyk commented 3 years ago

Actually, I think that in this case everything happened as planned. The config snippet I pasted is the result of setting alias identity with the server, which this part of the log hints at:

No local digest for genome alias: dm6
Setting 'dm6' identity with server: http://rg.databio.org/v3/alias/genome_digest/dm6
Determined server digest for local genome alias (dm6): 98190192e366fa1f69d56b75275b1064ec802a9cc85741d0
Set genome alias (98190192e366fa1f69d56b75275b1064ec802a9cc85741d0: dm6)

That would be also the result of calling:

[mstolarczyk@MichalsMBP refgenie]: refgenie alias set -a Ananas_comosus_JGI_v3_0 -f
Setting 'Ananas_comosus_JGI_v3_0' identity with server: http://plantref.databio.org/v3/alias/genome_digest/Ananas_comosus_JGI_v3_0
Determined server digest for local genome alias (Ananas_comosus_JGI_v3_0): 5980fd629d5a4b4418e42ba50f756ad0a0b29ea880ed67bf
Set genome alias (5980fd629d5a4b4418e42ba50f756ad0a0b29ea880ed67bf: Ananas_comosus_JGI_v3_0)
Created alias directories: 
 - /Users/mstolarczyk/Desktop/testing/refgenie/alias/Ananas_comosus_JGI_v3_0

This is an implementation of the setting genome identity with a server proposed here: https://github.com/refgenie/refgenie/issues/81#issue-468235395

Or to use a checksum straight from the server

refgenie alias -g hg38 This would also happen automatically on first pull, if the genome hasn't been initialized, syncing the identity with the server. All these do is add to the config file:

genomes: hg38: checksum: 64821b23d7a3c6bf42b697de48898110 description: blah blah blah

Now, when you pull -g hg38 ... it checks that checksum.